Esempio n. 1
0
/*----------------------------------------------------------------------------
 * Name:        h5rcreate_region_c
 * Purpose:     Call H5Rcreate to create a reference to dataset region
 *              region
 * Inputs:      loc_id - file or group identifier
 *              name - name of the dataset
 *              namelen - name length
 *              space_id - dataset space identifier
 * Outputs:     ref  - reference to the dataset region
 * Returns:     0 on success, -1 on failure
 * Programmer:  Elena Pourmal
 *              Wednesday, December 1, 1999
 * Modifications:
 *---------------------------------------------------------------------------*/
int_f
nh5rcreate_region_c (int_f *ref, hid_t_f *loc_id, _fcd name, int_f *namelen, hid_t_f *space_id)
{
     int ret_value = -1;
     hid_t c_loc_id;
     hid_t c_space_id;
     int ret_value_c;
     char *c_name;
     int c_namelen;
     hdset_reg_ref_t ref_c;

     /*
      * Convert FORTRAN name to C name
      */
     c_namelen = *namelen;
     c_name = (char *)HD5f2cstring(name, c_namelen);
     if (c_name == NULL) return ret_value;

     /*
      * Call H5Rcreate function.
      */
     c_loc_id = *loc_id;
     c_space_id = *space_id;
     ret_value_c = H5Rcreate(&ref_c, c_loc_id, c_name, H5R_DATASET_REGION, c_space_id);

     HDfree(c_name);
     if (ret_value_c >= 0) {
         HDmemcpy (ref, &ref_c, H5R_DSET_REG_REF_BUF_SIZE);
         ret_value = 0;
     }
     return ret_value;
}
Esempio n. 2
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/*----------------------------------------------------------------------------
 * Name:        h5rcreate_object_c
 * Purpose:     Call H5Rcreate to create a reference to an object
 * Inputs:      loc_id - file or group identifier
 *              name - name of the dataset
 *              namelen - name length
 * Outputs:     ref  - reference to the object
 * Returns:     0 on success, -1 on failure
 * Programmer:  Elena Pourmal
 *              Wednesday, December 1, 1999
 * Modifications:
 *---------------------------------------------------------------------------*/
int_f
nh5rcreate_object_c (haddr_t_f *ref, hid_t_f *loc_id, _fcd name, int_f *namelen)
{
     int ret_value = -1;
     hid_t c_loc_id;
     int ret_value_c;
     char *c_name;
     int c_namelen;
     hobj_ref_t ref_c;

     /*
      * Convert FORTRAN name to C name
      */
     c_namelen = *namelen;
     c_name = (char *)HD5f2cstring(name, c_namelen);
     if (c_name == NULL) return ret_value;

     /*
      * Call H5Rcreate function.
      */
     c_loc_id = *loc_id;
     ret_value_c = H5Rcreate(&ref_c, c_loc_id, c_name, H5R_OBJECT, -1);

     HDfree(c_name);
     if (ret_value_c >= 0)  {
         *ref=(haddr_t_f)ref_c;
         ret_value = 0;
     }

     return ret_value;
}
Esempio n. 3
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    void DCDataSet::createReference(hid_t refGroup,
            hid_t srcGroup,
            DCDataSet &srcDataSet)
    throw (DCException)
    {
        if (opened)
            throw DCException(getExceptionString("createReference: dataset is already open"));

        if (checkExistence && H5Lexists(refGroup, name.c_str(), H5P_LINK_ACCESS_DEFAULT))
            throw DCException(getExceptionString("createReference: this reference already exists"));

        getLogicalSize().set(srcDataSet.getLogicalSize());
        this->ndims = srcDataSet.getNDims();

        if (H5Rcreate(&regionRef, srcGroup, srcDataSet.getName().c_str(), H5R_OBJECT, -1) < 0)
            throw DCException(getExceptionString("createReference: failed to create region reference"));

        hsize_t ndims = 1;
        dataspace = H5Screate_simple(1, &ndims, NULL);
        if (dataspace < 0)
            throw DCException(getExceptionString("createReference: failed to create dataspace for reference"));

        dataset = H5Dcreate(refGroup, name.c_str(), H5T_STD_REF_OBJ,
                dataspace, H5P_DEFAULT, dsetProperties, H5P_DEFAULT);

        if (dataset < 0)
            throw DCException(getExceptionString("createReference: failed to create dataset for reference"));

        if (H5Dwrite(dataset, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL,
                dsetWriteProperties, &regionRef) < 0)
            throw DCException(getExceptionString("createReference: failed to write reference"));

        isReference = true;
        opened = true;
    }
Esempio n. 4
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//--------------------------------------------------------------------------
// Function:    H5Object::p_reference (protected)
// Purpose      Creates a reference to an HDF5 object or a dataset region.
// Parameters
//              name - IN: Name of the object to be referenced
//              dataspace - IN: Dataspace with selection
//              ref_type - IN: Type of reference; default to \c H5R_DATASET_REGION
// Exception    H5::IdComponentException
// Programmer   Binh-Minh Ribler - May, 2004
//--------------------------------------------------------------------------
void H5Object::p_reference(void* ref, const char* name, hid_t space_id, H5R_type_t ref_type) const
{
   herr_t ret_value = H5Rcreate(ref, getId(), name, ref_type, space_id);
   if (ret_value < 0)
   {
      throw IdComponentException("", "H5Rcreate failed");
   }
}
Esempio n. 5
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//--------------------------------------------------------------------------
// Function:	H5Location::p_reference (protected)
// Purpose	Creates a reference to an HDF5 object or a dataset region.
// Parameters
//		name - IN: Name of the object to be referenced
//		dataspace - IN: Dataspace with selection
//		ref_type - IN: Type of reference; default to \c H5R_DATASET_REGION
// Exception	H5::ReferenceException
// Programmer	Binh-Minh Ribler - May, 2004
//--------------------------------------------------------------------------
void H5Location::p_reference(void* ref, const char* name, hid_t space_id, H5R_type_t ref_type) const
{
   herr_t ret_value = H5Rcreate(ref, getId(), name, ref_type, space_id);
   if (ret_value < 0)
   {
      throw ReferenceException(inMemFunc("reference"), "H5Rcreate failed");
   }
}
Esempio n. 6
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void NSDFWriter::createEventMap()
{
    herr_t status;    
    hid_t eventMapContainer = require_group(filehandle_, MAPEVENTSRC);
    // Open the container for the event maps
    // Create the Datasets themselves (one for each field - each row
    // for one object).
    for (map< string, vector < string > >::iterator ii = classFieldToEventSrc_.begin();
         ii != classFieldToEventSrc_.end();
         ++ii){
        vector < string > pathTokens;
        tokenize(ii->first, "/", pathTokens);
        string className = pathTokens[0];
        string fieldName = pathTokens[1];
        hid_t classGroup = require_group(eventMapContainer, className);
        hid_t strtype = H5Tcopy(H5T_C_S1);
        status = H5Tset_size(strtype, H5T_VARIABLE);
        // create file space
        hid_t ftype = H5Tcreate(H5T_COMPOUND, sizeof(hvl_t) +sizeof(hobj_ref_t));
        status = H5Tinsert(ftype, "source", 0, strtype);
        status = H5Tinsert(ftype, "data", sizeof(hvl_t), H5T_STD_REF_OBJ);
        hsize_t dims[1] = {ii->second.size()};
        hid_t space = H5Screate_simple(1, dims, NULL);
        // The dataset for mapping is named after the field
        hid_t ds = H5Dcreate2(classGroup, fieldName.c_str(), ftype, space,
                              H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
        status = H5Sclose(space);
        map_type * buf = (map_type*)calloc(ii->second.size(), sizeof(map_type));
        // Populate the buffer entries with source uid and data
        // reference
        for (unsigned int jj = 0; jj < ii->second.size(); ++jj){
            buf->source = ii->second[jj].c_str();
            char * dsname = (char*)calloc(256, sizeof(char));
            ssize_t size = H5Iget_name(classFieldToEvent_[ii->first][jj], dsname, 255);
            if (size > 255){
                free(dsname);
                dsname = (char*)calloc(size, sizeof(char));
                size = H5Iget_name(classFieldToEvent_[ii->first][jj], dsname, 255);
            }
            status = H5Rcreate(&(buf->data), filehandle_, dsname, H5R_OBJECT, -1);
            free(dsname);
            assert(status >= 0);            
        }
        // create memory space
        hid_t memtype = H5Tcreate(H5T_COMPOUND, sizeof(map_type));
        status = H5Tinsert(memtype, "source",
                           HOFFSET(map_type, source), strtype);
        status = H5Tinsert(memtype, "data",
                           HOFFSET(map_type, data), H5T_STD_REF_OBJ);
        status = H5Dwrite(ds, memtype,  H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
        free(buf);
        status = H5Tclose(strtype);
        status = H5Tclose(ftype);
        status = H5Tclose(memtype);
        status = H5Dclose(ds);
    }
}
Esempio n. 7
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/*
 * Class:     hdf_hdf5lib_H5
 * Method:    H5Rcreate
 * Signature: ([BJLjava/lang/String;IJ)I
 */
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Rcreate(JNIEnv *env, jclass clss, jbyteArray ref, jlong loc_id, jstring name, jint ref_type, jlong space_id)
{
    const char *rName;
    herr_t      status = -1;
    jbyte      *refP;
    jboolean    isCopy2;

    PIN_JAVA_STRING(name, rName, -1);

    if (ref == NULL) {
        UNPIN_JAVA_STRING(name, rName);
        h5nullArgument( env, "H5Rcreate:  ref is NULL");
    } /* end if */
    else {
        if ((ref_type == H5R_OBJECT) && ENVPTR->GetArrayLength(ENVPAR ref) != H5R_OBJ_REF_BUF_SIZE) {
            UNPIN_JAVA_STRING(name, rName);
            h5badArgument( env, "H5Rcreate:  ref input array != H5R_OBJ_REF_BUF_SIZE");
        } /* end if */
        else if ((ref_type == H5R_DATASET_REGION) && ENVPTR->GetArrayLength(ENVPAR ref) != H5R_DSET_REG_REF_BUF_SIZE) {
            UNPIN_JAVA_STRING(name, rName);
            h5badArgument( env, "H5Rcreate:  region ref input array != H5R_DSET_REG_REF_BUF_SIZE");
        } /* end else if */
        else if ((ref_type != H5R_OBJECT) && (ref_type != H5R_DATASET_REGION)) {
            UNPIN_JAVA_STRING(name, rName);
            h5badArgument( env, "H5Rcreate:  ref_type unknown type ");
        } /* end else if */
        else {
            refP = (jbyte*)ENVPTR->GetByteArrayElements(ENVPAR ref, &isCopy2);
            if (refP == NULL) {
                UNPIN_JAVA_STRING(name, rName);
                h5JNIFatalError(env,  "H5Rcreate:  ref not pinned");
            } /* end if */
            else {
                status = H5Rcreate(refP, (hid_t)loc_id, rName, (H5R_type_t)ref_type, (hid_t)space_id);

                UNPIN_JAVA_STRING(name, rName);
                if (status < 0) {
                    ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, JNI_ABORT);
                    h5libraryError(env);
                } /* end if */
                else {
                    ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, 0);
                } /* end else */
            } /* end else */
        } /* end else */
    } /* end else */

    return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Rcreate */
Esempio n. 8
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    void DCDataSet::createReference(hid_t refGroup,
            hid_t srcGroup,
            DCDataSet &srcDataSet,
            Dimensions count,
            Dimensions offset,
            Dimensions stride)
    throw (DCException)
    {
        if (opened)
            throw DCException(getExceptionString("createReference: dataset is already open"));

        if (checkExistence && H5Lexists(refGroup, name.c_str(), H5P_LINK_ACCESS_DEFAULT))
            throw DCException(getExceptionString("createReference: this reference already exists"));

        getLogicalSize().set(count);
        this->ndims = srcDataSet.getNDims();

        count.swapDims(this->ndims);
        offset.swapDims(this->ndims);
        stride.swapDims(this->ndims);

        // select region hyperslab in source dataset
        if (H5Sselect_hyperslab(srcDataSet.getDataSpace(), H5S_SELECT_SET,
                offset.getPointer(), stride.getPointer(),
                count.getPointer(), NULL) < 0 ||
                H5Sselect_valid(srcDataSet.getDataSpace()) <= 0)
            throw DCException(getExceptionString("createReference: failed to select hyperslap for reference"));

        if (H5Rcreate(&regionRef, srcGroup, srcDataSet.getName().c_str(), H5R_DATASET_REGION,
                srcDataSet.getDataSpace()) < 0)
            throw DCException(getExceptionString("createReference: failed to create region reference"));

        hsize_t ndims = 1;
        dataspace = H5Screate_simple(1, &ndims, NULL);
        if (dataspace < 0)
            throw DCException(getExceptionString("createReference: failed to create dataspace for reference"));

        dataset = H5Dcreate(refGroup, name.c_str(), H5T_STD_REF_DSETREG,
                dataspace, H5P_DEFAULT, dsetProperties, H5P_DEFAULT);

        if (dataset < 0)
            throw DCException(getExceptionString("createReference: failed to create dataset for reference"));

        if (H5Dwrite(dataset, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL,
                dsetWriteProperties, &regionRef) < 0)
            throw DCException(getExceptionString("createReference: failed to write reference"));

        isReference = true;
        opened = true;
    }
Esempio n. 9
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int main(void)
{
    hid_t file_id;        /* file identifier */
    hid_t space_id;       /* dataspace identifiers */
    hid_t spacer_id;
    hid_t dsetv_id;       /*dataset identifiers*/
    hid_t dsetr_id;
    hsize_t dims[2] =  {2,9};
    hsize_t dimsr[1] =  {2};
    int rank = 2;
    int rankr =1;
    herr_t status;
    hdset_reg_ref_t ref[2];
    hdset_reg_ref_t ref_out[2];
    int data[2][9] = {{1,1,2,3,3,4,5,5,6},{1,2,2,3,4,4,5,6,6}};
    int data_out[2][9] = {{0,0,0,0,0,0,0,0,0},{0,0,0,0,0,0,0,0,0}};
    hsize_t start[2];
    hsize_t count[2];
    hsize_t coord[2][3] = {{0, 0, 1}, {6, 0, 8}};
    unsigned num_points = 3;
    int i, j;
    size_t name_size1, name_size2;
    char buf1[10], buf2[10];

    /*
     * Create file with default file access and file creation properties.
     */
    file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

    /*
     * Create dataspace for datasets.
     */
    space_id = H5Screate_simple(rank, dims, NULL);
    spacer_id = H5Screate_simple(rankr, dimsr, NULL);

    /*
     * Create integer dataset.
     */
    dsetv_id = H5Dcreate2(file_id, dsetnamev, H5T_NATIVE_INT, space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);

    /*
     * Write data to the dataset.
     */
    status = H5Dwrite(dsetv_id, H5T_NATIVE_INT, H5S_ALL , H5S_ALL, H5P_DEFAULT,data);
    status = H5Dclose(dsetv_id);

    /*
     * Dataset with references.
     */
    dsetr_id = H5Dcreate2(file_id, dsetnamer, H5T_STD_REF_DSETREG, spacer_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);

    /*
     * Create a reference to the hyperslab.
     */
    start[0] = 0;
    start[1] = 3;
    count[0] = 2;
    count[1] = 3;
    status = H5Sselect_hyperslab(space_id, H5S_SELECT_SET, start, NULL, count, NULL);
    status = H5Rcreate(&ref[0], file_id, dsetnamev, H5R_DATASET_REGION, space_id);

    /*
     * Create a reference to elements selection.
     */
    status = H5Sselect_none(space_id);
    status = H5Sselect_elements(space_id, H5S_SELECT_SET, num_points, (const hsize_t *)coord);
    status = H5Rcreate(&ref[1], file_id, dsetnamev, H5R_DATASET_REGION, space_id);

    /*
     * Write dataset with the references.
     */
    status = H5Dwrite(dsetr_id, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, H5P_DEFAULT,ref);

    /*
     * Close all objects.
     */
    status = H5Sclose(space_id);
    status = H5Sclose(spacer_id);
    status = H5Dclose(dsetr_id);
    status = H5Fclose(file_id);

    /*
     * Reopen the file to read selections back.
     */
    file_id = H5Fopen(filename, H5F_ACC_RDWR,  H5P_DEFAULT);

    /*
     * Reopen the dataset with object references and read references
     * to the buffer.
     */
    dsetr_id = H5Dopen2(file_id, dsetnamer, H5P_DEFAULT);

    status = H5Dread(dsetr_id, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL,
                   H5P_DEFAULT, ref_out);

    /*
     * Dereference the first reference.
     */
    dsetv_id = H5Rdereference2(dsetr_id, H5P_DEFAULT, H5R_DATASET_REGION, &ref_out[0]);
    /*
     * Get name of the dataset the first region reference points to
     * using H5Rget_name
     */
    name_size1 = H5Rget_name(dsetr_id, H5R_DATASET_REGION, &ref_out[0], (char*)buf1, 10);
    printf(" Dataset's name (returned by H5Rget_name) the reference points to is %s, name length is %d\n", buf1, (int)name_size1);
    /*
     * Get name of the dataset the first region reference points to
     * using H5Iget_name
     */
    name_size2 = H5Iget_name(dsetv_id, (char*)buf2, 10);
    printf(" Dataset's name (returned by H5Iget_name) the reference points to is %s, name length is %d\n", buf2, (int)name_size2);

    space_id = H5Rget_region(dsetr_id, H5R_DATASET_REGION,&ref_out[0]);

    /*
     * Read and display hyperslab selection from the dataset.
     */

    status = H5Dread(dsetv_id, H5T_NATIVE_INT, H5S_ALL, space_id,
                   H5P_DEFAULT, data_out);
    printf("Selected hyperslab: ");
    for (i = 0; i <= 1; i++)
    {
        printf("\n");
        for (j = 0; j <= 8; j++)
            printf("%d ", data_out[i][j]);
    }
    printf("\n");

    /*
     * Close dataspace and the dataset.
     */
    status = H5Sclose(space_id);
    status = H5Dclose(dsetv_id);

    /*
     * Initialize data_out array again to get point selection.
     */
    for (i = 0; i <= 1; i++)
        for (j = 0; j <= 8; j++)
            data_out[i][j] = 0;

    /*
     * Dereference the second reference.
     */
    dsetv_id = H5Rdereference2(dsetr_id, H5P_DEFAULT, H5R_DATASET_REGION, &ref_out[1]);
    space_id = H5Rget_region(dsetv_id, H5R_DATASET_REGION,&ref_out[1]);

    /*
     * Read selected data from the dataset.
     */

    status = H5Dread(dsetv_id, H5T_NATIVE_INT, H5S_ALL, space_id,
                   H5P_DEFAULT, data_out);
    printf("Selected points: ");
    for (i = 0; i <= 1; i++)
    {
        printf("\n");
        for (j = 0; j <= 8; j++)
            printf("%d ", data_out[i][j]);
    }
    printf("\n");

    /*
     * Close dataspace and the dataset.
     */
    status = H5Sclose(space_id);
    status = H5Dclose(dsetv_id);
    status = H5Dclose(dsetr_id);
    status = H5Fclose(file_id);

    return 0;
}
Esempio n. 10
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int
main(void) {
   hid_t fid;                         /* File, group, datasets, datatypes */
   hid_t gid_a;                       /* and  dataspaces identifiers   */
   hid_t did_b, sid_b, tid_b;
   hid_t did_r, tid_r, sid_r;
   H5O_type_t obj_type;
   herr_t status;

   hobj_ref_t *wbuf; /* buffer to write to disk */
   hobj_ref_t *rbuf; /* buffer to read from disk */


   hsize_t dim_r[1];
   hsize_t dim_b[2];

   /*
    *  Create a file using default properties.
    */
   fid = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

   /*
    *  Create  group "A" in the file.
    */
   gid_a = H5Gcreate2(fid, "A", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);

  /*
   *  Create dataset "B" in the file.
   */
   dim_b[0] = 2;
   dim_b[1] = 6;
   sid_b = H5Screate_simple(2, dim_b, NULL);
   did_b = H5Dcreate2(fid, "B", H5T_NATIVE_FLOAT, sid_b, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);

   /*
    *  Create dataset "R" to store references to the objects "A" and "B".
    */
   dim_r[0] = 2;
   sid_r = H5Screate_simple(1, dim_r, NULL);
   tid_r = H5Tcopy(H5T_STD_REF_OBJ);
   did_r = H5Dcreate2(fid, "R", tid_r, sid_r, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);

   /*
    *  Allocate write and read buffers.
    */
   wbuf = (hobj_ref_t *)malloc(sizeof(hobj_ref_t) * 2);
   rbuf = (hobj_ref_t *)malloc(sizeof(hobj_ref_t) * 2);

   /*
    *  Create references to the group "A" and dataset "B"
    *  and store them in the wbuf.
    */
   H5Rcreate(&wbuf[0], fid, "A", H5R_OBJECT, (hid_t)-1);
   H5Rcreate(&wbuf[1], fid, "B", H5R_OBJECT, (hid_t)-1);

   /*
    *  Write dataset R using default transfer properties.
    */
   status = H5Dwrite(did_r, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, wbuf);

   /*
    *  Close all objects.
    */
   H5Gclose(gid_a);

   H5Sclose(sid_b);
   H5Dclose(did_b);

   H5Tclose(tid_r);
   H5Sclose(sid_r);
   H5Dclose(did_r);

   H5Fclose(fid);

   /*
    * Reopen the file.
    */
   fid = H5Fopen(H5FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT);

   /*
    *  Open and read dataset "R".
    */
   did_r  = H5Dopen2(fid, "R", H5P_DEFAULT);
   status = H5Dread(did_r, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, rbuf);

   /*
    * Find the type of referenced objects.
    */
    status = H5Rget_obj_type2(did_r, H5R_OBJECT, &rbuf[0], &obj_type);
    if(obj_type == H5O_TYPE_GROUP)
        printf("First dereferenced object is a group. \n");

    status = H5Rget_obj_type2(did_r, H5R_OBJECT, &rbuf[1], &obj_type);
    if(obj_type == H5O_TYPE_DATASET)
        printf("Second dereferenced object is a dataset. \n");

   /*
    *  Get datatype of the dataset "B"
    */
   did_b = H5Rdereference2(did_r, H5P_DEFAULT, H5R_OBJECT, &rbuf[1]);
   tid_b = H5Dget_type(did_b);
   if(H5Tequal(tid_b, H5T_NATIVE_FLOAT))
     printf("Datatype of the dataset is H5T_NATIVE_FLOAT.\n");
   printf("\n");

   /*
    * Close all objects and free memory buffers.
    */
   H5Dclose(did_r);
   H5Dclose(did_b);
   H5Tclose(tid_b);
   H5Fclose(fid);
   free(rbuf);
   free(wbuf);

   return 0;
 }
Esempio n. 11
0
/*****************************************************************************
  This function generates attributes, groups, and datasets of many types. 

  Parameters:
            fname:	file_name.
            ngrps:	number of top level groups.
            ndsets:	number of datasets.
            attrs:	number of attributes.
            nrow:	number of rows in a dataset.
            chunk:	chunk size (single number).
            vlen:	max vlen size.
            comp:	use latest format.
            latest:	use gzip comnpression.
			
  Return:  Non-negative on success/Negative on failure
  
  Programmer:  Peter Cao <*****@*****.**>, Jan. 2013
 ****************************************************************************/
herr_t create_perf_test_file(const char *fname, int ngrps, int ndsets, 
       int nattrs, hsize_t nrows, hsize_t dim0, hsize_t chunk, int vlen, 
	   int compressed, int latest)
{
    int         i, j, k;
    hid_t       fid, sid_null, sid_scalar, sid_1d, sid_2d, did, aid, sid_2, sid_large, 
	            fapl=H5P_DEFAULT, dcpl=H5P_DEFAULT, gid1, gid2, cmp_tid, tid_str, 
				tid_enum, tid_array_f, tid_vlen_i, tid_vlen_s;
    char        name[32], tmp_name1[32], tmp_name2[32], tmp_name3[32];
    hsize_t     dims[1]={dim0}, dims2d[2]={dim0, (dim0/4+1)}, dims_array[1]={FIXED_LEN}, 
	            dim1[1]={2};
    char        *enum_names[4] = {"SOLID", "LIQUID", "GAS", "PLASMA"};
    test_comp_t *buf_comp=NULL, *buf_comp_large=NULL;
    int         *buf_int=NULL;
    float       (*buf_float_a)[FIXED_LEN]=NULL;
    double      **buf_double2d=NULL;
    hvl_t       *buf_vlen_i=NULL;
	char        (*buf_str)[FIXED_LEN];
	char        **buf_vlen_s=NULL;
	hobj_ref_t  buf_ref[2];
	hdset_reg_ref_t buf_reg_ref[2];
    size_t      offset, len;
    herr_t      status;
    char        *names[NTYPES] = { "int", "ulong", "float", "double", "fixed string", 
	            "enum", "fixed float array", "vlen int array", "vlen strings"};
    hid_t       types[NTYPES] = { H5T_NATIVE_INT, H5T_NATIVE_UINT64, H5T_NATIVE_FLOAT, 
                H5T_NATIVE_DOUBLE, tid_str, tid_enum, tid_array_f, tid_vlen_i, tid_vlen_s};
	hsize_t     coords[4][2] = { {0,  1}, {3, 5}, {1,  0}, {2,  4}}, start=0, stride=1, count=1;
	
	if (nrows < NROWS) nrows = NROWS; 
    if (ngrps<NGROUPS) ngrps=NGROUPS;
	if (ndsets<NDSETS) ndsets=NDSETS;
	if (nattrs<NATTRS) nattrs=NATTRS;
	if (dim0<DIM0) dim0=DIM0;
    if (chunk>dim0) chunk=dim0/4;
    if (chunk<1) chunk = 1;
	if (vlen<1) vlen = MAXVLEN;

    /* create fixed string datatype */                                   
    types[4] = tid_str =  H5Tcopy (H5T_C_S1);
    H5Tset_size (tid_str, FIXED_LEN);

    /* create enum datatype */
    types[5] = tid_enum = H5Tenum_create(H5T_NATIVE_INT);
    for (i = (int) SOLID; i <= (int) PLASMA; i++) {
        phase_t val = (phase_t) i;
        status = H5Tenum_insert (tid_enum, enum_names[i], &val);
    }

    /* create float array datatype */
    types[6] = tid_array_f = H5Tarray_create (H5T_NATIVE_FLOAT, 1, dims_array);
 
    /* create variable length integer datatypes */
    types[7] = tid_vlen_i = H5Tvlen_create (H5T_NATIVE_INT);
    	
    /* create variable length string datatype */
    types[8] = tid_vlen_s =  H5Tcopy (H5T_C_S1);
    H5Tset_size (tid_vlen_s, H5T_VARIABLE);
                   
    /* create compound datatypes */    
    cmp_tid = H5Tcreate (H5T_COMPOUND, sizeof (test_comp_t));
    offset = 0;
    for (i=0; i<NTYPES-2; i++) {
        H5Tinsert(cmp_tid, names[i], offset, types[i]);
        offset += H5Tget_size(types[i]);
    }

	H5Tinsert(cmp_tid, names[7], offset, types[7]);
	offset += sizeof (hvl_t);
	H5Tinsert(cmp_tid, names[8], offset, types[8]);

	/* create dataspace */
    sid_1d = H5Screate_simple (1, dims, NULL);
    sid_2d = H5Screate_simple (2, dims2d, NULL);
    sid_2 = H5Screate_simple  (1, dim1, NULL);
	sid_large = H5Screate_simple  (1, &nrows, NULL);
    sid_null = H5Screate (H5S_NULL);	
	sid_scalar = H5Screate (H5S_SCALAR);
	
	/* create fid access property */
	fapl = H5Pcreate (H5P_FILE_ACCESS);
    H5Pset_libver_bounds (fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST);

	/* create dataset creation property */
    dcpl = H5Pcreate (H5P_DATASET_CREATE);

	/* set dataset chunk */
    if (chunk>0) {
        H5Pset_chunk (dcpl, 1, &chunk);
    }

	/* set dataset compression */
    if (compressed) {
        if (chunk<=0) {
            chunk = dim0/10+1;;
            H5Pset_chunk (dcpl, 1, &chunk);
        }
        H5Pset_shuffle (dcpl);
        H5Pset_deflate (dcpl, 6);
    }	

	/* allocate buffers */
    buf_comp   = (test_comp_t *)calloc(dim0, sizeof(test_comp_t));
    buf_comp_large   = (test_comp_t *)calloc(nrows, sizeof(test_comp_t));
    buf_int    = (int *)calloc(dim0, sizeof(int));
    buf_float_a  = malloc(dim0*sizeof(*buf_float_a));
	buf_vlen_i = (hvl_t *)calloc(dim0, sizeof (hvl_t));
    buf_vlen_s = (char **)calloc(dim0, sizeof(char *));
	buf_str    =  malloc(dim0*sizeof (*buf_str));

	/* allocate array of doulbe pointers */
	buf_double2d  = (double **)calloc(dims2d[0],sizeof(double *));
	/* allocate a contigous chunk of memory for the data */
	buf_double2d[0] = (double *)calloc( dims2d[0]*dims2d[1],sizeof(double) );
	/* assign memory city to pointer array */
	for (i=1; i <dims2d[0]; i++) buf_double2d[i] = buf_double2d[0]+i*dims2d[1];

	/* fill buffer values */
	len = 1;
    for (i=0; i<dims[0]; i++) {
        buf_comp[i].i = buf_int[i] = i-2147483648;
        buf_comp[i].l = 0xffffffffffffffff-i;
        buf_comp[i].f = 1.0/(i+1.0);
        buf_comp[i].d = 987654321.0*i+1.0/(i+1.0);
        buf_comp[i].e = (phase_t) (i % (int) (PLASMA + 1));
		
		for (j=0; j<FIXED_LEN; j++) {
		    buf_comp[i].f_array[j] = buf_float_a[i][j] = i*100+j;
			buf_str[i][j] = 'a' + (i%26);
		}
		buf_str[i][FIXED_LEN-1] = 0;
        strcpy(buf_comp[i].s, buf_str[i]);
		
		len = (1-cos(i/8.0))/2*vlen+1;
		if (!i) len = vlen;
		buf_vlen_i[i].len = len;
		buf_vlen_i[i].p = (int *)calloc(len, sizeof(int));
		for (j=0; j<len; j++) ((int*)(buf_vlen_i[i].p))[j] = i*100+j;
		buf_comp[i].i_vlen = buf_vlen_i[i];
		
		buf_vlen_s[i] = (char *)calloc(len, sizeof(char));
		for (j=0; j<len-1; j++)
		    buf_vlen_s[i][j] = j%26+'A';
		buf_comp[i].s_vlen = buf_vlen_s[i];
		
		for (j=0; j<dims2d[1]; j++)
		    buf_double2d[i][j] = i+j/10000.0;
    }

    for (i=0; i<nrows; i++) {
        buf_comp_large[i].i = i-2147483648;
        buf_comp_large[i].l = 0xffffffffffffffff-i;
        buf_comp_large[i].f = 1.0/(i+1.0);
        buf_comp_large[i].d = 987654321.0*i+1.0/(i+1.0);
        buf_comp_large[i].e = (phase_t) (i % (int) (PLASMA + 1));
        for (j=0; j<FIXED_LEN-1; j++) {
            buf_comp_large[i].f_array[j] = i*100+j;
            buf_comp_large[i].s[j] = 'a' + (i%26);
        }
		len = i%vlen+1;
        buf_comp_large[i].i_vlen.len = len;
        buf_comp_large[i].i_vlen.p = (int *)calloc(len, sizeof(int));
        for (j=0; j<len; j++) ((int*)(buf_comp_large[i].i_vlen.p))[j] = i*100+j;
        buf_comp_large[i].s_vlen = (char *)calloc(i+2, sizeof(char));
        for (j=0; j<i+1; j++) (buf_comp_large[i].s_vlen)[j] = j%26+'A';
    }
	
	/* create file */
    if (latest)
        fid = H5Fcreate (fname, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
    else
        fid = H5Fcreate (fname, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
	add_attrs(fid, 0);

	sprintf(name, "a cmp ds of %d rows", nrows);
	did = H5Dcreate (fid, name, cmp_tid, sid_large, H5P_DEFAULT, dcpl, H5P_DEFAULT);
	H5Dwrite (did, cmp_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_comp_large);
	add_attrs(did, 0); 
	H5Dclose(did);

	// /* add attributes*/
    gid1 = H5Gcreate (fid, "attributes", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
	if (nattrs<1) nattrs = 1;
	i=0;
	while (i<nattrs) i += add_attrs(gid1, i);
	H5Gclose(gid1);
		
	/* add many sub groups to a group*/
    gid1 = H5Gcreate (fid, "groups", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
	add_attrs(gid1, 0);
    for (i=0; i<ngrps; i++) {
	    /* create sub groups */
        sprintf(name, "g%02d", i);
        gid2 = H5Gcreate (gid1, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
		if (i<10) add_attrs(gid2, 0);
		H5Gclose(gid2);
	}
	H5Gclose(gid1);

	/* add many datasets to a group */
	gid1 = H5Gcreate (fid, "datasets", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
	add_attrs(gid1, 0);
    for (j=0; j<ndsets; j+=12) {
		/* 1 add a null dataset */
		sprintf(name, "%05d null dataset", j);
        did = H5Dcreate (gid1, name, H5T_STD_I32LE, sid_null, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
		if (!j) add_attrs(did, j); 
        H5Dclose(did);	

		/* 2 add scalar int point */
	    sprintf(name, "%05d scalar int point", j);
        did = H5Dcreate (gid1, name, H5T_NATIVE_INT, sid_scalar, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
        H5Dwrite (did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &j);		
		if (!j) add_attrs(did, j); 
		H5Dclose(did);		
		
		/* 3 scalar vlen string */
	    sprintf(name, "%05d scalar vlen string", j);
        did = H5Dcreate (gid1, name, tid_vlen_s, sid_scalar, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
        H5Dwrite (did, tid_vlen_s, H5S_ALL, H5S_ALL, H5P_DEFAULT, &buf_vlen_s[0]);		
		if (!j) add_attrs(did, j); 
		H5Dclose(did);			
	
	    /* 4 add fixed-length float array */
		sprintf(name, "%05d fixed-length float array", j);
		did = H5Dcreate (gid1, name, tid_array_f, sid_1d, H5P_DEFAULT, dcpl, H5P_DEFAULT);
		H5Dwrite (did, tid_array_f, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_float_a);
		if (!j) add_attrs(did, j); 
		H5Dclose(did);
	
		/* 5 add fixed-length strings */
		sprintf(name, "%05d fixed-length strings", j);
		did = H5Dcreate (gid1, name, tid_str, sid_1d, H5P_DEFAULT, dcpl, H5P_DEFAULT);
		H5Dwrite (did, tid_str, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_str);
		if (!j) add_attrs(did, j); 
		H5Dclose(did);
		
		/* 6 add compound data */
	    sprintf(name, "%05d compund data", j);
	    did = H5Dcreate (gid1, name, cmp_tid, sid_1d, H5P_DEFAULT, dcpl, H5P_DEFAULT);
	    H5Dwrite (did, cmp_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_comp);
		if (!j) add_attrs(did, j); 
		H5Dclose(did);

		/* 7 add 2D double */
	    sprintf(name, "%05d 2D double", j);
		strcpy (tmp_name1, name);
	    did = H5Dcreate (gid1, name, H5T_NATIVE_DOUBLE, sid_2d, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
	    H5Dwrite (did, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_double2d[0]);
		if (!j) add_attrs(did, j); 
		H5Dclose(did);
		
		/* 8 add 1D int array */
	    sprintf(name, "%05d 1D int array", j);
        did = H5Dcreate (gid1, name, H5T_NATIVE_INT, sid_1d, H5P_DEFAULT, dcpl, H5P_DEFAULT);
        H5Dwrite (did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_int);		
		if (!j) add_attrs(did, j); 
		H5Dclose(did);
		
		/* 9 add vlen int array */
	    sprintf(name, "%05d vlen int array", j);
		strcpy (tmp_name2, name);
        did = H5Dcreate (gid1, name, tid_vlen_i, sid_1d, H5P_DEFAULT, dcpl, H5P_DEFAULT);
        H5Dwrite (did, tid_vlen_i, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_vlen_i);		
		if (!j) add_attrs(did, j); 
		H5Dclose(did);	

		/* 10 add vlen strings */
	    sprintf(name, "%05d vlen strings", j);
		strcpy (tmp_name3, name);
        did = H5Dcreate (gid1, name, tid_vlen_s, sid_1d, H5P_DEFAULT, dcpl, H5P_DEFAULT);
        H5Dwrite (did, tid_vlen_s, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_vlen_s);		
		if (!j) add_attrs(did, j); 
		H5Dclose(did);	
		
		/* 11 add object refs */
		H5Rcreate(&buf_ref[0],gid1, ".", H5R_OBJECT, -1); 
		H5Rcreate(&buf_ref[1],gid1, tmp_name3, H5R_OBJECT, -1); 
	    sprintf(name, "%05d obj refs", j);
        did = H5Dcreate (gid1, name, H5T_STD_REF_OBJ, sid_2, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
        H5Dwrite (did, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_ref);		
		if (!j) add_attrs(did, j); 
		H5Dclose(did);

		/* 12 add region refs */
		H5Sselect_elements (sid_2d, H5S_SELECT_SET, 4, coords[0]);
		H5Rcreate(&buf_reg_ref[0],gid1, tmp_name1, H5R_DATASET_REGION, sid_2d); 
		H5Sselect_none(sid_2d);
		count = dims[0]/2+1;
		H5Sselect_hyperslab (sid_1d, H5S_SELECT_SET, &start, &stride, &count,NULL);
		H5Rcreate(&buf_reg_ref[1],gid1, tmp_name2, H5R_DATASET_REGION, sid_1d); 
		H5Sselect_none(sid_1d);
	    sprintf(name, "%05d region refs", j);
        did = H5Dcreate (gid1, name, H5T_STD_REF_DSETREG, sid_2, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
        H5Dwrite (did, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_reg_ref);		
		if (!j) add_attrs(did, j); 
		H5Dclose(did);
	}
	H5Gclose(gid1);			
	
    H5Tclose (tid_array_f);
    H5Tclose (tid_vlen_i);
    H5Tclose (tid_vlen_s);
    H5Tclose (tid_enum);
    H5Tclose (tid_str);
    H5Tclose (cmp_tid);
    H5Pclose (dcpl);
    H5Pclose (fapl);
    H5Sclose (sid_1d);
    H5Sclose (sid_2d);
    H5Sclose (sid_2);
    H5Sclose (sid_large);
    H5Sclose (sid_null);
    H5Sclose (sid_scalar);
    H5Fclose (fid);

    for (i=0; i<dims[0]; i++) {
		if (buf_vlen_i[i].p) free(buf_vlen_i[i].p);
		if (buf_vlen_s[i]) free(buf_vlen_s[i]);
	}

    for (i=0; i<nrows; i++) {
	    if (buf_comp_large[i].i_vlen.p)  free(buf_comp_large[i].i_vlen.p);
		if (buf_comp_large[i].s_vlen) free(buf_comp_large[i].s_vlen);
	}
	
    free (buf_comp);
    free (buf_comp_large);
    free (buf_int);
    free (buf_float_a);
    free (buf_double2d[0]);
    free (buf_double2d);
	free (buf_str);
    free(buf_vlen_i);
    free(buf_vlen_s);

    return 0;
}
Esempio n. 12
0
/* 
    adds different types of attributes to an object.
	
	returns the number of attributes added to the objects.
 */
int add_attrs(hid_t oid, int idx) 
{
    char name[32];
    int i0, i1, i2, j, nattrs=0;
	hid_t aid, tid, tid1, sid;
    hvl_t               i_vlen[4];
	hobj_ref_t          ref;
	zipcode_t            cmp_data[4];
    unsigned int        i = 0xffffffff;
    long long           l = -2147483647;
    float               f = 123456789.987654321;
    double              d = 987654321.123456789;
    char                *s[7] = {"Parting", "is such", "sweeter", "sorrow."};
    float               f_array[4] = {1.0, 2.22, 3.333, 4.444};
    char                *s_vlen[4] = {"Parting", "is such", "sweet", "sorrow."};
	hsize_t             dims1[1]={1}, dims2[1]={4}, dims3[2]={3,5};
	int                 int3d[4][3][5];
	 size_t             offset = 0;
	
	for (i0=0; i0<4; i0++) {
	    i_vlen[i0].len = (i0+1);
		i_vlen[i0].p = (int *)calloc(i_vlen[i0].len, sizeof(int));
		for (j=0; j<i_vlen[i0].len; j++)
		    ((int *)i_vlen[i0].p)[j] = i0*100+j;
	    for (i1=0; i1<3; i1++) {
	        for (i2=0; i2<5; i2++)
	            int3d[i0][i1][i2] = i0*i1-i1*i2+i0*i2;
		}
    }

	cmp_data[0].zipcode = 01001;
    cmp_data[0].city = "Agawam, Massachusetts";
    cmp_data[1].zipcode = 99950;
    cmp_data[1].city = "Ketchikan, Alaska";
    cmp_data[2].zipcode = 00501;
    cmp_data[2].city = "Holtsville, New York";
    cmp_data[3].zipcode = 61820;
    cmp_data[3].city = "Champaign, Illinois";
	
	/* 1 scalar point */
	sid = H5Screate (H5S_SCALAR);
	sprintf(name, "%05d scalar int", idx);
    nattrs += add_attr(oid, name, H5T_NATIVE_UINT, sid, &i);	
	sprintf(name, "%05d scalar ulong", idx);
    nattrs += add_attr(oid, name, H5T_NATIVE_INT64, sid, &l);	
	sprintf(name, "%05d scalar str", idx);
	tid =  H5Tcopy (H5T_C_S1);
    H5Tset_size (tid, H5T_VARIABLE);
    nattrs += add_attr(oid, name, tid, sid, &s[2]);	
	H5Tclose(tid);
	H5Sclose(sid);

	/* 4 single point */
	sid = H5Screate_simple (1, dims1, NULL);
    H5Rcreate(&ref, oid, ".", H5R_OBJECT, -1);
	sprintf(name, "%05d single float", idx);
    nattrs += add_attr(oid, name, H5T_NATIVE_FLOAT, sid, &f);	
	sprintf(name, "%05d single double", idx);
    nattrs += add_attr(oid, name, H5T_NATIVE_DOUBLE, sid, &d);	
	sprintf(name, "%05d single obj_ref", idx);
    nattrs += add_attr(oid, name, H5T_STD_REF_OBJ, sid, &ref);	
	H5Sclose(sid);
	
	/* 7 fixed length 1D array */
	sid = H5Screate_simple (1, dims1, NULL);
	tid = H5Tarray_create (H5T_NATIVE_FLOAT, 1, dims2);
	sprintf(name, "%05d array float", idx);
    nattrs += add_attr(oid, name, tid, sid, &f_array[0]);
	H5Tclose(tid);
	tid =  H5Tcopy (H5T_C_S1);
    H5Tset_size (tid, strlen(s[0])+1);	
	tid1 = H5Tarray_create (tid, 1, dims2);
	sprintf(name, "%05d array str", idx);
    nattrs += add_attr(oid, name, tid1, sid, s);	
	H5Tclose(tid1);	
	H5Tclose(tid);	
	H5Sclose(sid);

	/* 9 fixed length 2D int arrays */
	sid = H5Screate_simple (1, dims2, NULL);
	tid = H5Tarray_create (H5T_NATIVE_INT, 2, dims3);
	sprintf(name, "%05d array int 2D", idx);
    nattrs += add_attr(oid, name, tid, sid, int3d[0][0]);
	H5Tclose(tid);
	H5Sclose(sid);
	
	/* 10 variable length arrays */
	sid = H5Screate_simple (1, dims2, NULL);
	tid = H5Tcopy (H5T_C_S1);
	H5Tset_size (tid, H5T_VARIABLE);
	sprintf(name, "%05d vlen strings", idx);
    nattrs += add_attr(oid, name, tid, sid, s_vlen);
	H5Tclose(tid);	
	tid = H5Tvlen_create (H5T_NATIVE_INT);;
	sprintf(name, "%05d vlen int array", idx);
    nattrs += add_attr(oid, name, tid, sid, i_vlen);
	H5Tclose(tid);
	H5Sclose(sid);

	/* 12 compound data */
	sid = H5Screate_simple (1, dims2, NULL);
	tid = H5Tcreate (H5T_COMPOUND, sizeof (zipcode_t));
	tid1 = H5Tcopy (H5T_C_S1);
	H5Tset_size (tid1, H5T_VARIABLE);	
    H5Tinsert (tid, "zip code", 0, H5T_NATIVE_INT); offset += sizeof(H5T_NATIVE_INT);
    H5Tinsert (tid, "City", offset, tid1); offset += sizeof(char *);
	sprintf(name, "%05d compound data", idx);
    nattrs += add_attr(oid, name, tid, sid, cmp_data);
	H5Tclose(tid1);	
	H5Tclose(tid);	
	H5Sclose(sid);

	for (i0=0; i0<4; i0++) 
	    free(i_vlen[i0].p);
		
	return nattrs;
}
Esempio n. 13
0
herr_t H5IMlink_palette( hid_t loc_id,
                        const char *image_name,
                        const char *pal_name )

{
    hid_t       did;
    hid_t       atid=-1;
    hid_t       aid=-1;
    hid_t       asid=-1;
    hobj_ref_t  ref;         /* write a new reference */
    hobj_ref_t  *refbuf;     /* buffer to read references */
    hssize_t    n_refs;
    hsize_t     dim_ref;
    int         ok_pal;

    
    /* check the arguments */
    if (image_name == NULL) 
      return -1;
    if (pal_name == NULL) 
      return -1;

    /* The image dataset may or may not have the attribute "PALETTE"
    * First we try to open to see if it is already there; if not, it is created.
    * If it exists, the array of references is extended to hold the reference
    * to the new palette
    */

    /* First we get the image id */
    if((did = H5Dopen2(loc_id, image_name, H5P_DEFAULT)) < 0)
        return -1;

    /* Try to find the attribute "PALETTE" on the >>image<< dataset */
    ok_pal = H5LT_find_attribute( did, "PALETTE" );

    /*-------------------------------------------------------------------------
    * It does not exist. We create the attribute and one reference
    *-------------------------------------------------------------------------
    */
    if(ok_pal == 0 )
    {
        if((asid = H5Screate(H5S_SCALAR)) < 0)
            goto out;

        /* Create the attribute type for the reference */
        if((atid = H5Tcopy(H5T_STD_REF_OBJ)) < 0)
            goto out;

        /* Create the attribute "PALETTE" to be attached to the image*/
        if((aid = H5Acreate2(did, "PALETTE", atid, asid, H5P_DEFAULT, H5P_DEFAULT)) < 0)
            goto out;

        /* Create a reference. The reference is created on the local id.  */
        if(H5Rcreate(&ref, loc_id, pal_name, H5R_OBJECT, (hid_t)-1) < 0)
            goto out;

        /* Write the attribute with the reference */
        if(H5Awrite(aid, atid, &ref) < 0)
            goto out;

        /* close */
        if(H5Sclose(asid) < 0)
            goto out;
        if(H5Tclose(atid) < 0)
            goto out;
        if(H5Aclose(aid) < 0)
            goto out;

    }

    /*-------------------------------------------------------------------------
    * The attribute already exists, open it
    *-------------------------------------------------------------------------
    */
    else if(ok_pal ==  1)
    {
        if((aid = H5Aopen(did, "PALETTE", H5P_DEFAULT)) < 0)
            goto out;

        if((atid = H5Aget_type(aid)) < 0)
            goto out;

        if(H5Tget_class(atid) < 0)
            goto out;

        /* Get and save the old reference(s) */
        if((asid = H5Aget_space(aid)) < 0)
            goto out;

        n_refs = H5Sget_simple_extent_npoints(asid);

        dim_ref = (hsize_t)n_refs + 1;

        refbuf = (hobj_ref_t*)HDmalloc( sizeof(hobj_ref_t) * (size_t)dim_ref );

        if ( H5Aread( aid, atid, refbuf ) < 0)
            goto out;

        /* The attribute must be deleted, in order to the new one can reflect the changes*/
        if(H5Adelete(did, "PALETTE") < 0)
            goto out;

        /* Create a new reference for this palette. */
        if ( H5Rcreate( &ref, loc_id, pal_name, H5R_OBJECT, (hid_t)-1 ) < 0)
            goto out;

        refbuf[n_refs] = ref;

        /* Create the data space for the new references */
        if(H5Sclose(asid) < 0)
            goto out;

        if((asid = H5Screate_simple(1, &dim_ref, NULL)) < 0)
            goto out;

        /* Create the attribute again with the changes of space */
        if(H5Aclose(aid) < 0)
            goto out;

        if((aid = H5Acreate2(did, "PALETTE", atid, asid, H5P_DEFAULT, H5P_DEFAULT)) < 0)
            goto out;

        /* Write the attribute with the new references */
        if(H5Awrite(aid, atid, refbuf) < 0)
            goto out;

        /* close */
        if(H5Sclose(asid) < 0)
            goto out;
        if(H5Tclose(atid) < 0)
            goto out;
        if(H5Aclose(aid) < 0)
            goto out;

        HDfree( refbuf );

    } /* ok_pal ==  1 */

    /* Close the image dataset. */
    if ( H5Dclose( did ) < 0)
        return -1;

    return 0;

out:
    H5Dclose( did );
    H5Sclose( asid );
    H5Tclose( atid );
    H5Aclose( aid );
    return -1;
}
Esempio n. 14
0
int
main (void)
{
    hid_t       file, space, dset, obj, attr;   /* Handles */
    herr_t      status;
    hsize_t     dims[1] = {DIM0};
    hobj_ref_t  wdata[DIM0],                    /* Write buffer */
                *rdata;                         /* Read buffer */
    H5G_obj_t   objtype;
    ssize_t     size;
    char        *name;
    int         ndims,
                i;

    /*
     * Create a new file using the default properties.
     */
    file = H5Fcreate (FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

    /*
     * Create a dataset with a scalar dataspace.
     */
    space = H5Screate (H5S_SCALAR);
    obj = H5Dcreate (file, "DS2", H5T_STD_I32LE, space, H5P_DEFAULT);
    status = H5Dclose (obj);
    status = H5Sclose (space);

    /*
     * Create a group.
     */
    obj = H5Gcreate (file, "G1", H5P_DEFAULT);
    status = H5Gclose (obj);

    /*
     * Create references to the previously created objects.  Passing -1
     * as space_id causes this parameter to be ignored.  Other values
     * besides valid dataspaces result in an error.
     */
    status = H5Rcreate (&wdata[0], file, "G1", H5R_OBJECT, -1);
    status = H5Rcreate (&wdata[1], file, "DS2", H5R_OBJECT, -1);

    /*
     * Create dataset with a scalar dataspace to serve as the parent
     * for the attribute.
     */
    space = H5Screate (H5S_SCALAR);
    dset = H5Dcreate (file, DATASET, H5T_STD_I32LE, space, H5P_DEFAULT);
    status = H5Sclose (space);

    /*
     * Create dataspace.  Setting maximum size to NULL sets the maximum
     * size to be the current size.
     */
    space = H5Screate_simple (1, dims, NULL);

    /*
     * Create the attribute and write the object references to it.
     */
    attr = H5Acreate (dset, ATTRIBUTE, H5T_STD_REF_OBJ, space, H5P_DEFAULT);
    status = H5Awrite (attr, H5T_STD_REF_OBJ, wdata);

    /*
     * Close and release resources.
     */
    status = H5Aclose (attr);
    status = H5Dclose (dset);
    status = H5Sclose (space);
    status = H5Fclose (file);


    /*
     * Now we begin the read section of this example.  Here we assume
     * the attribute has the same name and rank, but can have any size.
     * Therefore we must allocate a new array to read in data using
     * malloc().
     */

    /*
     * Open file, dataset, and attribute.
     */
    file = H5Fopen (FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
    dset = H5Dopen (file, DATASET);
    attr = H5Aopen_name (dset, ATTRIBUTE);

    /*
     * Get dataspace and allocate memory for read buffer.
     */
    space = H5Aget_space (attr);
    ndims = H5Sget_simple_extent_dims (space, dims, NULL);
    rdata = (hobj_ref_t *) malloc (dims[0] * sizeof (hobj_ref_t));

    /*
     * Read the data.
     */
    status = H5Aread (attr, H5T_STD_REF_OBJ, rdata);

    /*
     * Output the data to the screen.
     */
    for (i=0; i<dims[0]; i++) {
        printf ("%s[%d]:\n  ->", ATTRIBUTE, i);

        /*
         * Open the referenced object, get its name and type.
         */
        obj = H5Rdereference (dset, H5R_OBJECT, &rdata[i]);
        objtype = H5Rget_obj_type (dset, H5R_OBJECT, &rdata[i]);

        /*
         * Get the length of the name, allocate space, then retrieve
         * the name.
         */
        size = 1 + H5Iget_name (obj, NULL, 0);
        if (size > 1) {
            name = (char *) malloc (size);
            size = 1 + H5Iget_name (obj, name, size);
        }

        /*
         * Print the object type and close the object.
         */
        switch (objtype) {
            case H5G_GROUP:
                printf ("Group");
                status = H5Gclose (obj);
                break;
            case H5G_DATASET:
                printf ("Dataset");
                status = H5Dclose (obj);
                break;
            case H5G_TYPE:
                printf ("Named Datatype");
                status = H5Tclose (obj);
        }

        /*
         * Print the name and deallocate space for the name.
         */
        if (size > 1) {
            printf (": %s", name);
            free (name);
        }
        printf ("\n");
    }

    /*
     * Close and release resources.
     */
    free (rdata);
    status = H5Aclose (attr);
    status = H5Dclose (dset);
    status = H5Sclose (space);
    status = H5Fclose (file);

    return 0;
}
Esempio n. 15
0
/*-------------------------------------------------------------------------
 * Function: gen_region_ref
 *
 * Purpose: Generate dataset region references
 *
 * Programmer: Jonathan Kim (Feb 23, 2010)
 *------------------------------------------------------------------------*/
static herr_t gen_region_ref(hid_t loc_id)
{
    hid_t sid=0, oid1=0, oid2=0;
    int status;
    herr_t ret = SUCCEED;
    char  data[3][16] = {"The quick brown", "fox jumps over ", "the 5 lazy dogs"};
    hsize_t dims2[2] = {3,16};
    hsize_t coords[4][2] = { {0,1}, {2,11}, {1,0}, {2,4} };
    hdset_reg_ref_t  rr_data[2];
    hsize_t start[2] = {0,0};
    hsize_t stride[2] = {2,11};
    hsize_t count[2] = {2,2};
    hsize_t block[2] = {1,3};
    hsize_t dims1[1] = {2};

    sid = H5Screate_simple (2, dims2, NULL);
    if (sid < 0)
    {
        fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
        ret = FAIL;
        goto out;
    }

    /* create normal dataset which is refered */
    oid2 = H5Dcreate2 (loc_id, REG_REF_DS2, H5T_STD_I8LE, sid, H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
    if (oid2 < 0)
    {
        fprintf(stderr, "Error: %s %d> H5Dcreate2 failed.\n", FUNC, __LINE__);
        ret = FAIL;
        goto out;
    }

    /* write values to dataset */
    status = H5Dwrite (oid2, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
    if (status < 0)
    {
        fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
        ret = FAIL;
        goto out;
    }

    /* select elements space for reference */
    status = H5Sselect_elements (sid, H5S_SELECT_SET, 4, coords[0]);
    if (status < 0)
    {
        fprintf(stderr, "Error: %s %d> H5Sselect_elements failed.\n", FUNC, __LINE__);
        ret = FAIL;
        goto out;
    }

    /* create region reference from elements space */
    status = H5Rcreate (&rr_data[0], loc_id, REG_REF_DS2, H5R_DATASET_REGION, sid);
    if (status < 0)
    {
        fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
        ret = FAIL;
        goto out;
    }

    /* select hyperslab space for reference */
    status = H5Sselect_hyperslab (sid, H5S_SELECT_SET, start, stride, count, block);
    if (status < 0)
    {
        fprintf(stderr, "Error: %s %d> H5Sselect_hyperslab failed.\n", FUNC, __LINE__);
        ret = FAIL;
        goto out;
    }

    /* create region reference from hyperslab space */
    status = H5Rcreate (&rr_data[1], loc_id, REG_REF_DS2, H5R_DATASET_REGION, sid);
    if (status < 0)
    {
        fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
        ret = FAIL;
        goto out;
    }

    H5Sclose (sid);

    /* Create dataspace. */
    sid = H5Screate_simple (1, dims1, NULL);
    if (sid < 0)
    {
        fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
        ret = FAIL;
        goto out;
    }

    /* create region reference dataset */
    oid1 = H5Dcreate2 (loc_id, REG_REF_DS1, H5T_STD_REF_DSETREG, sid, H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
    if (oid1 < 0)
    {
        fprintf(stderr, "Error: %s %d> H5Dcreate2 failed.\n", FUNC, __LINE__);
        ret = FAIL;
        goto out;
    }

    /* write data as region references */
    status = H5Dwrite (oid1, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, H5P_DEFAULT, rr_data);
    if (status < 0)
    {
        fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
        ret = FAIL;
        goto out;
    }

out:
    if (oid1 > 0)
        H5Dclose (oid1);
    if (oid2 > 0)
        H5Dclose (oid2);
    if (sid > 0)
        H5Sclose (sid);

    return ret;
}
Esempio n. 16
0
/*-------------------------------------------------------------------------
 * Function: gen_obj_ref
 *
 * Purpose: Generate object references to dataset and group
 *
 * Programmer: Jonathan Kim (Feb 23, 2010)
 *------------------------------------------------------------------------*/
static herr_t gen_obj_ref(hid_t loc_id)
{
    hid_t sid=0, oid=0;
    hsize_t dims1[1]={3};
    hsize_t dims2[1]={2};
    int data[3] = {10,20,30};
    int status;

    /*---------------------
     * create obj references to the previously created objects.
     * Passing -1 as reference is an object.*/
    hobj_ref_t or_data[2];  /* write buffer */
    herr_t ret = SUCCEED;

    /*--------------
     * add dataset */
    sid = H5Screate_simple(1, dims1, NULL);
    if (sid < 0)
    {
        fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
        ret = FAIL;
        goto out;
    }

    oid = H5Dcreate2 (loc_id, OBJ_REF_DS, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
    if (oid < 0)
    {
        fprintf(stderr, "Error: %s %d> H5Dcreate2 failed.\n", FUNC, __LINE__);
        ret = FAIL;
        goto out;
    }

    status = H5Dwrite(oid, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
    if (status < 0)
    {
        fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
        ret = FAIL;
        goto out;
    }

    H5Dclose(oid);
    H5Sclose(sid);

    /*--------------
     * add group  */
     oid = H5Gcreate2 (loc_id, OBJ_REF_GRP, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
    if (oid < 0)
    {
        fprintf(stderr, "Error: %s %d> H5Gcreate2 failed.\n", FUNC, __LINE__);
        ret = FAIL;
        goto out;
    }
     H5Gclose(oid);

    status = H5Rcreate (&or_data[0], loc_id, OBJ_REF_DS, H5R_OBJECT, -1);
    if (status < 0)
    {
        fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
        ret = FAIL;
        goto out;
    }
    status = H5Rcreate (&or_data[1], loc_id, OBJ_REF_GRP, H5R_OBJECT, -1);
    if (status < 0)
    {
        fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
        ret = FAIL;
        goto out;
    }

    sid = H5Screate_simple (1, dims2, NULL);
    if (sid < 0)
    {
        fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
        ret = FAIL;
        goto out;
    }

    oid = H5Dcreate2 (loc_id, "Dset_OBJREF", H5T_STD_REF_OBJ, sid, H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
    if (oid < 0)
    {
        fprintf(stderr, "Error: %s %d> H5Dcreate2 failed.\n", FUNC, __LINE__);
        ret = FAIL;
        goto out;
    }

    status = H5Dwrite(oid, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, or_data);
    if (status < 0)
    {
        fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
        ret = FAIL;
        goto out;
    }

out:
    if(oid > 0)
        H5Dclose(oid);
    if(sid > 0)
        H5Sclose(sid);

    return ret;
}
Esempio n. 17
0
int 
main(void) {
    hid_t		fid1;		/* HDF5 File IDs		*/
    hid_t		dataset;	/* Dataset ID			*/
    hid_t		group;      /* Group ID             */
    hid_t		sid1;       /* Dataspace ID			*/
    hid_t		tid1;       /* Datatype ID			*/
    hsize_t		dims1[] = {SPACE1_DIM1};
    hobj_ref_t      *wbuf;      /* buffer to write to disk */
    int       *tu32;      /* Temporary pointer to int data */
    int        i;          /* counting variables */
    const char *write_comment="Foo!"; /* Comments for group */
    herr_t		ret;		/* Generic return value		*/

/* Compound datatype */
typedef struct s1_t {
    unsigned int a;
    unsigned int b;
    float c;
} s1_t;

    /* Allocate write buffers */
    wbuf=(hobj_ref_t *)malloc(sizeof(hobj_ref_t)*SPACE1_DIM1);
    tu32=malloc(sizeof(int)*SPACE1_DIM1);

    /* Create file */
    fid1 = H5Fcreate(FILE1, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

    /* Create dataspace for datasets */
    sid1 = H5Screate_simple(SPACE1_RANK, dims1, NULL);

    /* Create a group */
    group=H5Gcreate(fid1,"Group1",-1);

    /* Set group's comment */
    ret=H5Gset_comment(group,".",write_comment);

    /* Create a dataset (inside Group1) */
    dataset=H5Dcreate(group,"Dataset1",H5T_STD_U32LE,sid1,H5P_DEFAULT);

    for(i=0; i<SPACE1_DIM1; i++)
        tu32[i] = i*3;

    /* Write selection to disk */
    ret=H5Dwrite(dataset,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,tu32);

    /* Close Dataset */
    ret = H5Dclose(dataset);

    /* Create another dataset (inside Group1) */
    dataset=H5Dcreate(group,"Dataset2",H5T_NATIVE_UCHAR,sid1,H5P_DEFAULT);

    /* Close Dataset */
    ret = H5Dclose(dataset);

    /* Create a datatype to refer to */
    tid1 = H5Tcreate (H5T_COMPOUND, sizeof(s1_t));

    /* Insert fields */
    ret=H5Tinsert (tid1, "a", HOFFSET(s1_t,a), H5T_NATIVE_INT);

    ret=H5Tinsert (tid1, "b", HOFFSET(s1_t,b), H5T_NATIVE_INT);

    ret=H5Tinsert (tid1, "c", HOFFSET(s1_t,c), H5T_NATIVE_FLOAT);

    /* Save datatype for later */
    ret=H5Tcommit (group, "Datatype1", tid1);

    /* Close datatype */
    ret = H5Tclose(tid1);

    /* Close group */
    ret = H5Gclose(group);

    /* Create a dataset to store references */
    dataset=H5Dcreate(fid1,"Dataset3",H5T_STD_REF_OBJ,sid1,H5P_DEFAULT);

    /* Create reference to dataset */
    ret = H5Rcreate(&wbuf[0],fid1,"/Group1/Dataset1",H5R_OBJECT,-1);

    /* Create reference to dataset */
    ret = H5Rcreate(&wbuf[1],fid1,"/Group1/Dataset2",H5R_OBJECT,-1);

    /* Create reference to group */
    ret = H5Rcreate(&wbuf[2],fid1,"/Group1",H5R_OBJECT,-1);

    /* Create reference to named datatype */
    ret = H5Rcreate(&wbuf[3],fid1,"/Group1/Datatype1",H5R_OBJECT,-1);

    /* Write selection to disk */
    ret=H5Dwrite(dataset,H5T_STD_REF_OBJ,H5S_ALL,H5S_ALL,H5P_DEFAULT,wbuf);

    /* Close disk dataspace */
    ret = H5Sclose(sid1);
    
    /* Close Dataset */
    ret = H5Dclose(dataset);

    /* Close file */
    ret = H5Fclose(fid1);
    free(wbuf);
    free(tu32);
    return 0;
}
Esempio n. 18
0
int
main (void)
{
    hid_t               file, space, memspace, dset, dset2, attr;
                                                    /* Handles */
    herr_t              status;
    hsize_t             dims[1] = {DIM0},
                        dims2[2] = {DS2DIM0, DS2DIM1},
                        coords[4][2] = { {0,  1},
                                         {2, 11},
                                         {1,  0},
                                         {2,  4} },
                        start[2] = {0, 0},
                        stride[2] = {2, 11},
                        count[2] = {2, 2},
                        block[2] = {1, 3};
    hssize_t            npoints;
    hdset_reg_ref_t     wdata[DIM0],                /* Write buffer */
                        *rdata;                     /* Read buffer */
    ssize_t             size;
    char                wdata2[DS2DIM0][DS2DIM1] = {"The quick brown",
                                                    "fox jumps over ",
                                                    "the 5 lazy dogs"},
                        *rdata2,
                        *name;
    int                 ndims,
                        i;

    /*
     * Create a new file using the default properties.
     */
    file = H5Fcreate (FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

    /*
     * Create a dataset with character data.
     */
    space = H5Screate_simple (2, dims2, NULL);
    dset2 = H5Dcreate (file, DATASET2, H5T_STD_I8LE, space, H5P_DEFAULT,
                H5P_DEFAULT, H5P_DEFAULT);
    status = H5Dwrite (dset2, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL, H5P_DEFAULT,
                wdata2);

    /*
     * Create reference to a list of elements in dset2.
     */
    status = H5Sselect_elements (space, H5S_SELECT_SET, 4, coords[0]);
    status = H5Rcreate (&wdata[0], file, DATASET2, H5R_DATASET_REGION, space);

    /*
     * Create reference to a hyperslab in dset2, close dataspace.
     */
    status = H5Sselect_hyperslab (space, H5S_SELECT_SET, start, stride, count,
                block);
    status = H5Rcreate (&wdata[1], file, DATASET2, H5R_DATASET_REGION, space);
    status = H5Sclose (space);

    /*
     * Create dataset with a null dataspace to serve as the parent for
     * the attribute.
     */
    space = H5Screate (H5S_NULL);
    dset = H5Dcreate (file, DATASET, H5T_STD_I32LE, space, H5P_DEFAULT,
                H5P_DEFAULT, H5P_DEFAULT);
    status = H5Sclose (space);

    /*
     * Create dataspace.  Setting maximum size to NULL sets the maximum
     * size to be the current size.
     */
    space = H5Screate_simple (1, dims, NULL);

    /*
     * Create the attribute and write the region references to it.
     */
    attr = H5Acreate (dset, ATTRIBUTE, H5T_STD_REF_DSETREG, space, H5P_DEFAULT,
                    H5P_DEFAULT);
    status = H5Awrite (attr, H5T_STD_REF_DSETREG, wdata);

    /*
     * Close and release resources.
     */
    status = H5Aclose (attr);
    status = H5Dclose (dset);
    status = H5Dclose (dset2);
    status = H5Sclose (space);
    status = H5Fclose (file);


    /*
     * Now we begin the read section of this example.  Here we assume
     * the attribute has the same name and rank, but can have any size.
     * Therefore we must allocate a new array to read in data using
     * malloc().
     */

    /*
     * Open file, dataset, and attribute.
     */
    file = H5Fopen (FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
    dset = H5Dopen (file, DATASET, H5P_DEFAULT);
    attr = H5Aopen (dset, ATTRIBUTE, H5P_DEFAULT);

    /*
     * Get dataspace and allocate memory for read buffer.
     */
    space = H5Aget_space (attr);
    ndims = H5Sget_simple_extent_dims (space, dims, NULL);
    rdata = (hdset_reg_ref_t *) malloc (dims[0] * sizeof (hdset_reg_ref_t));
    status = H5Sclose (space);

    /*
     * Read the data.
     */
    status = H5Aread (attr, H5T_STD_REF_DSETREG, rdata);

    /*
     * Output the data to the screen.
     */
    for (i=0; i<dims[0]; i++) {
        printf ("%s[%d]:\n  ->", ATTRIBUTE, i);

        /*
         * Open the referenced object, retrieve its region as a
         * dataspace selection.
         */
        dset2 = H5Rdereference (dset, H5P_DEFAULT, H5R_DATASET_REGION, &rdata[i]);
        space = H5Rget_region (dset, H5R_DATASET_REGION, &rdata[i]);

        /*
         * Get the length of the object's name, allocate space, then
         * retrieve the name.
         */
        size = 1 + H5Iget_name (dset2, NULL, 0);
        name = (char *) malloc (size);
        size = H5Iget_name (dset2, name, size);

        /*
         * Allocate space for the read buffer.  We will only allocate
         * enough space for the selection, plus a null terminator.  The
         * read buffer will be 1-dimensional.
         */
        npoints = H5Sget_select_npoints (space);
        rdata2 = (char *) malloc (npoints + 1);

        /*
         * Read the dataset region, and add a null terminator so we can
         * print it as a string.
         */
        memspace = H5Screate_simple (1, (hsize_t *) &npoints, NULL);
        status = H5Dread (dset2, H5T_NATIVE_CHAR, memspace, space, H5P_DEFAULT,
                    rdata2);
        rdata2[npoints] = '\0';

        /*
         * Print the name and region data, close and release resources.
         */
        printf (" %s: %s\n", name, rdata2);
        free (rdata2);
        free (name);
        status = H5Sclose (space);
        status = H5Sclose (memspace);
        status = H5Dclose (dset2);
    }

    /*
     * Close and release resources.
     */
    free (rdata);
    status = H5Aclose (attr);
    status = H5Dclose (dset);
    status = H5Fclose (file);

    return 0;
}
Esempio n. 19
0
 ObjectReference Object::reference () const {
   ObjectReference ref;
   Exception::check ("H5Rcreate", H5Rcreate (&ref.value (), handle (), ".", H5R_OBJECT, -1));
   return ref;
 }
Esempio n. 20
0
int do_copy_refobjs(hid_t fidin,
                    hid_t fidout,
                    trav_table_t *travt,
                    pack_opt_t *options) /* repack options */
{
    hid_t     grp_in=(-1);            /* read group ID */
    hid_t     grp_out=(-1);           /* write group ID */
    hid_t     dset_in=(-1);           /* read dataset ID */
    hid_t     dset_out=(-1);          /* write dataset ID */
    hid_t     type_in=(-1);           /* named type ID */
    hid_t     dcpl_id=(-1);           /* dataset creation property list ID */
    hid_t     space_id=(-1);          /* space ID */
    hid_t     ftype_id=(-1);          /* file data type ID */
    hid_t     mtype_id=(-1);          /* memory data type ID */
    size_t    msize;                  /* memory size of memory type */
    hsize_t   nelmts;                 /* number of elements in dataset */
    int       rank;                   /* rank of dataset */
    hsize_t   dims[H5S_MAX_RANK];     /* dimensions of dataset */
    unsigned int i, j;
    int       k;
    
    /*-------------------------------------------------------------------------
    * browse
    *-------------------------------------------------------------------------
    */
    
    for ( i = 0; i < travt->nobjs; i++)
    {
        switch ( travt->objs[i].type )
        {
        /*-------------------------------------------------------------------------
        * H5G_GROUP
        *-------------------------------------------------------------------------
        */
        case H5G_GROUP:
            
        /*-------------------------------------------------------------------------
        * copy referenced objects in attributes
        *-------------------------------------------------------------------------
        */
            
            if ((grp_out=H5Gopen(fidout,travt->objs[i].name))<0)
                goto error;
            if((grp_in = H5Gopen (fidin,travt->objs[i].name))<0)
                goto error;
            if (copy_refs_attr(grp_in,grp_out,options,travt,fidout)<0)
                goto error;
            if (H5Gclose(grp_out)<0)
                goto error;
            if (H5Gclose(grp_in)<0)
                goto error;
            
           /*-------------------------------------------------------------------------
            * check for hard links
            *-------------------------------------------------------------------------
            */
            
            if (travt->objs[i].nlinks)
            {
                for ( j=0; j<travt->objs[i].nlinks; j++)
                {
                    H5Glink(fidout,
                        H5G_LINK_HARD,
                        travt->objs[i].name,
                        travt->objs[i].links[j].new_name);
                }
            }
            
            break;
            
       /*-------------------------------------------------------------------------
       * H5G_DATASET
       *-------------------------------------------------------------------------
       */
        case H5G_DATASET:
            
            if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0)
                goto error;
            if ((space_id=H5Dget_space(dset_in))<0)
                goto error;
            if ((ftype_id=H5Dget_type (dset_in))<0)
                goto error;
            if ((dcpl_id=H5Dget_create_plist(dset_in))<0)
                goto error;
            if ( (rank=H5Sget_simple_extent_ndims(space_id))<0)
                goto error;
            if ( H5Sget_simple_extent_dims(space_id,dims,NULL)<0)
                goto error;
            nelmts=1;
            for (k=0; k<rank; k++)
                nelmts*=dims[k];
            
            if ((mtype_id=h5tools_get_native_type(ftype_id))<0)
                goto error;
            
            if ((msize=H5Tget_size(mtype_id))==0)
                goto error;
            
            
           /*-------------------------------------------------------------------------
           * check if the dataset creation property list has filters that
           * are not registered in the current configuration
           * 1) the external filters GZIP and SZIP might not be available
           * 2) the internal filters might be turned off
           *-------------------------------------------------------------------------
           */
            if (h5tools_canreadf((NULL),dcpl_id)==1)
            {
               /*-------------------------------------------------------------------------
                * test for a valid output dataset
                *-------------------------------------------------------------------------
                */
                dset_out = FAIL;
                
                /*-------------------------------------------------------------------------
                * object references are a special case
                * we cannot just copy the buffers, but instead we recreate the reference
                *-------------------------------------------------------------------------
                */
                if (H5Tequal(mtype_id, H5T_STD_REF_OBJ))
                {
                    H5G_obj_t1       obj_type;
                    hid_t            refobj_id;
                    hobj_ref_t       *refbuf=NULL; /* buffer for object references */
                    hobj_ref_t       *buf=NULL;
                    const char*      refname;
                    unsigned         u;
                    
                    /*-------------------------------------------------------------------------
                    * read to memory
                    *-------------------------------------------------------------------------
                    */
                    
                    if (nelmts)
                    {
                        buf=(void *) HDmalloc((unsigned)(nelmts*msize));
                        if ( buf==NULL){
                            printf( "cannot read into memory\n" );
                            goto error;
                        }
                        if (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
                            goto error;
                        
                        if ((obj_type = H5Rget_obj_type(dset_in,H5R_OBJECT,buf))<0)
                            goto error;
                        refbuf=HDcalloc((unsigned)nelmts,msize);
                        if ( refbuf==NULL){
                            printf( "cannot allocate memory\n" );
                            goto error;
                        }
                        for ( u=0; u<nelmts; u++)
                        {
                            H5E_BEGIN_TRY {
                                if ((refobj_id = H5Rdereference(dset_in,H5R_OBJECT,&buf[u]))<0)
                                    continue;
                            } H5E_END_TRY;
                            /* get the name. a valid name could only occur in the
                            second traversal of the file */
                            if ((refname=MapIdToName(refobj_id,travt))!=NULL)
                            {
                                /* create the reference, -1 parameter for objects */
                                if (H5Rcreate(&refbuf[u],fidout,refname,H5R_OBJECT,-1)<0)
                                    goto error;
                                if(options->verbose)
                                {
                                    
                                    
                                    printf(FORMAT_OBJ,"dset",travt->objs[i].name );
                                    printf("object <%s> object reference created to <%s>\n",
                                        travt->objs[i].name,
                                        refname);
                                }
                            }/*refname*/
                            close_obj(obj_type,refobj_id);
                        }/*  u */
                    }/*nelmts*/
                    
                     /*-------------------------------------------------------------------------
                     * create/write dataset/close
                     *-------------------------------------------------------------------------
                    */
                    if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,mtype_id,space_id,dcpl_id))<0)
                        goto error;
                    if (nelmts) {
                        if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
                            goto error;
                    }
                    
                    if (buf)
                        free(buf);
                    if (refbuf)
                        free(refbuf);
                    
                }/*H5T_STD_REF_OBJ*/
                
                 /*-------------------------------------------------------------------------
                 * dataset region references
                 *-------------------------------------------------------------------------
                */
                else if (H5Tequal(mtype_id, H5T_STD_REF_DSETREG))
                {
                    H5G_obj_t1       obj_type;
                    hid_t            refobj_id;
                    hdset_reg_ref_t  *refbuf=NULL; /* input buffer for region references */
                    hdset_reg_ref_t  *buf=NULL;    /* output buffer */
                    const char*      refname;
                    unsigned         u;
                    
                    /*-------------------------------------------------------------------------
                    * read input to memory
                    *-------------------------------------------------------------------------
                    */
                    if (nelmts)
                    {
                        buf=(void *) HDmalloc((unsigned)(nelmts*msize));
                        if ( buf==NULL){
                            printf( "cannot read into memory\n" );
                            goto error;
                        }
                        if (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
                            goto error;
                        if ((obj_type = H5Rget_obj_type(dset_in,H5R_DATASET_REGION,buf))<0)
                            goto error;
                        
                        /*-------------------------------------------------------------------------
                        * create output
                        *-------------------------------------------------------------------------
                        */
                        
                        refbuf=HDcalloc(sizeof(hdset_reg_ref_t),(size_t)nelmts); /*init to zero */
                        if ( refbuf==NULL){
                            printf( "cannot allocate memory\n" );
                            goto error;
                        }
                        for ( u=0; u<nelmts; u++)
                        {
                            H5E_BEGIN_TRY {
                                if ((refobj_id = H5Rdereference(dset_in,H5R_DATASET_REGION,&buf[u]))<0)
                                    continue;
                            } H5E_END_TRY;
                            
                            /* get the name. a valid name could only occur in the
                            second traversal of the file */
                            if ((refname=MapIdToName(refobj_id,travt))!=NULL)
                            {
                                hid_t region_id;    /* region id of the referenced dataset */
                                if ((region_id = H5Rget_region(dset_in,H5R_DATASET_REGION,&buf[u]))<0)
                                    goto error;
                                /* create the reference, we need the space_id */
                                if (H5Rcreate(&refbuf[u],fidout,refname,H5R_DATASET_REGION,region_id)<0)
                                    goto error;
                                if (H5Sclose(region_id)<0)
                                    goto error;
                                if(options->verbose)
                                {
                                    
                                    
                                    
                                    printf(FORMAT_OBJ,"dset",travt->objs[i].name );
                                    printf("object <%s> region reference created to <%s>\n",
                                        travt->objs[i].name,
                                        refname);
                                }
                            }/*refname*/
                            close_obj(obj_type,refobj_id);
                        }/*  u */
                    }/*nelmts*/
                    
                     /*-------------------------------------------------------------------------
                     * create/write dataset/close
                     *-------------------------------------------------------------------------
                    */
                    if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,mtype_id,space_id,dcpl_id))<0)
                        goto error;
                    if (nelmts) {
                        if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
                            goto error;
                    }
                    
                    if (buf)
                        free(buf);
                    if (refbuf)
                        free(refbuf);
                } /* H5T_STD_REF_DSETREG */
                
                
               /*-------------------------------------------------------------------------
                * not references, open previously created object in 1st traversal
                *-------------------------------------------------------------------------
                */
                else
                {
                    if ((dset_out=H5Dopen(fidout,travt->objs[i].name))<0)
                        goto error;
                }
                
                assert(dset_out!=FAIL);
                
                /*-------------------------------------------------------------------------
                * copy referenced objects in attributes
                *-------------------------------------------------------------------------
                */
                if (copy_refs_attr(dset_in,dset_out,options,travt,fidout)<0)
                    goto error;
                
                
                /*-------------------------------------------------------------------------
                * check for hard links
                *-------------------------------------------------------------------------
                */
                if (travt->objs[i].nlinks)
                {
                    for ( j=0; j<travt->objs[i].nlinks; j++){
                        H5Glink(fidout,
                            H5G_LINK_HARD,
                            travt->objs[i].name,
                            travt->objs[i].links[j].new_name);
                    }
                }
                
                if (H5Dclose(dset_out)<0)
                    goto error;
                
   }/*can_read*/
Esempio n. 21
0
/*
 * test_objnames
 * Tests that UTF-8 can be used for object names in the file.
 * Tests groups, datasets, named datatypes, and soft links.
 * Note that this test doesn't actually mark the names as being
 * in UTF-8.  At the time this test was written, that feature
 * didn't exist in HDF5, and when the character encoding property
 * was added to links it didn't change how they were stored in the file,
 * -JML 2/2/2006
 */
void test_objnames(hid_t fid, const char* string)
{
  hid_t grp_id, grp1_id, grp2_id, grp3_id;
  hid_t type_id, dset_id, space_id;
  char read_buf[MAX_STRING_LENGTH];
  char path_buf[MAX_PATH_LENGTH];
  hsize_t dims=1;
  hobj_ref_t obj_ref;
  herr_t ret;

  /* Create a group with a UTF-8 name */
  grp_id = H5Gcreate2(fid, string, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
  CHECK(grp_id, FAIL, "H5Gcreate2");

  /* Set a comment on the group to test that we can access the group
   * Also test that UTF-8 comments can be read.
   */
  ret = H5Oset_comment_by_name(fid, string, string, H5P_DEFAULT);
  CHECK(ret, FAIL, "H5Oset_comment_by_name");
  ret = H5Oget_comment_by_name(fid, string, read_buf, (size_t)MAX_STRING_LENGTH, H5P_DEFAULT);
  CHECK(ret, FAIL, "H5Oget_comment_by_name");

  ret = H5Gclose(grp_id);
  CHECK(ret, FAIL, "H5Gclose");

  VERIFY(HDstrcmp(string, read_buf), 0, "strcmp");

  /* Create a new dataset with a UTF-8 name */
  grp1_id = H5Gcreate2(fid, GROUP1_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
  CHECK(grp1_id, FAIL, "H5Gcreate2");

  space_id = H5Screate_simple(RANK, &dims, NULL);
  CHECK(space_id, FAIL, "H5Screate_simple");
  dset_id = H5Dcreate2(grp1_id, string, H5T_NATIVE_INT, space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
  CHECK(dset_id, FAIL, "H5Dcreate2");

  /* Make sure that dataset can be opened again */
  ret = H5Dclose(dset_id);
  CHECK(ret, FAIL, "H5Dclose");
  ret = H5Sclose(space_id);
  CHECK(ret, FAIL, "H5Sclose");

  dset_id = H5Dopen2(grp1_id, string, H5P_DEFAULT);
  CHECK(ret, FAIL, "H5Dopen2");
  ret = H5Dclose(dset_id);
  CHECK(ret, FAIL, "H5Dclose");
  ret = H5Gclose(grp1_id);
  CHECK(ret, FAIL, "H5Gclose");

  /* Do the same for a named datatype */
  grp2_id = H5Gcreate2(fid, GROUP2_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
  CHECK(grp2_id, FAIL, "H5Gcreate2");

  type_id = H5Tcreate(H5T_OPAQUE, (size_t)1);
  CHECK(type_id, FAIL, "H5Tcreate");
  ret = H5Tcommit2(grp2_id, string, type_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
  CHECK(type_id, FAIL, "H5Tcommit2");
  ret = H5Tclose(type_id);
  CHECK(type_id, FAIL, "H5Tclose");

  type_id = H5Topen2(grp2_id, string, H5P_DEFAULT);
  CHECK(type_id, FAIL, "H5Topen2");
  ret = H5Tclose(type_id);
  CHECK(type_id, FAIL, "H5Tclose");

  /* Don't close the group -- use it to test that object references
   * can refer to objects named in UTF-8 */

  space_id = H5Screate_simple(RANK, &dims, NULL);
  CHECK(space_id, FAIL, "H5Screate_simple");
  dset_id = H5Dcreate2(grp2_id, DSET3_NAME, H5T_STD_REF_OBJ, space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
  CHECK(ret, FAIL, "H5Dcreate2");

  /* Create reference to named datatype */
  ret = H5Rcreate(&obj_ref, grp2_id, string, H5R_OBJECT, -1);
  CHECK(ret, FAIL, "H5Rcreate");
  /* Write selection and read it back*/
  ret = H5Dwrite(dset_id, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, &obj_ref);
  CHECK(ret, FAIL, "H5Dwrite");
  ret = H5Dread(dset_id, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, &obj_ref);
  CHECK(ret, FAIL, "H5Dread");

  /* Ensure that we can open named datatype using object reference */
  type_id = H5Rdereference2(dset_id, H5P_DEFAULT, H5R_OBJECT, &obj_ref);
  CHECK(type_id, FAIL, "H5Rdereference2");
  ret = H5Tcommitted(type_id);
  VERIFY(ret, 1, "H5Tcommitted");

  ret = H5Tclose(type_id);
  CHECK(type_id, FAIL, "H5Tclose");
  ret = H5Dclose(dset_id);
  CHECK(ret, FAIL, "H5Dclose");
  ret = H5Sclose(space_id);
  CHECK(ret, FAIL, "H5Sclose");

  ret = H5Gclose(grp2_id);
  CHECK(ret, FAIL, "H5Gclose");

  /* Create "group3".  Build a hard link from group3 to group2, which has
   * a datatype with the UTF-8 name.  Create a soft link in group3
   * pointing through the hard link to the datatype.  Give the soft
   * link a name in UTF-8.  Ensure that the soft link works. */

  grp3_id = H5Gcreate2(fid, GROUP3_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
  CHECK(grp3_id, FAIL, "H5Gcreate2");

  ret = H5Lcreate_hard(fid, GROUP2_NAME, grp3_id, GROUP2_NAME, H5P_DEFAULT, H5P_DEFAULT);
  CHECK(ret, FAIL, "H5Lcreate_hard");
  HDstrcpy(path_buf, GROUP2_NAME);
  HDstrcat(path_buf, "/");
  HDstrcat(path_buf, string);
  ret = H5Lcreate_hard(grp3_id, path_buf, H5L_SAME_LOC, string, H5P_DEFAULT, H5P_DEFAULT);
  CHECK(ret, FAIL, "H5Lcreate_hard");

  /* Open named datatype using soft link */
  type_id = H5Topen2(grp3_id, string, H5P_DEFAULT);
  CHECK(type_id, FAIL, "H5Topen2");

  ret = H5Tclose(type_id);
  CHECK(type_id, FAIL, "H5Tclose");
  ret = H5Gclose(grp3_id);
  CHECK(ret, FAIL, "H5Gclose");
}